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http://purl.bioontology.org/ontology/ORDO

Ontology to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (http://www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).

Proper citation: Orphanet Rare Disease Ontology (RRID:SCR_010402) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/PEO

Ontology that models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway.

Proper citation: Parasite Experiment Ontology (RRID:SCR_010403) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/PHARE

Ontology that proposes concepts and roles to represent relationships of pharmacogenomics interest.

Proper citation: Pharmacogenomic Relationships Ontology (RRID:SCR_010406) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Genomon-Project

Software DNA and RNA sequence analysis pipeline.

Proper citation: GenomonPipeline (RRID:SCR_022989) Copy   

•   Source: SciCrunch Registry
  

http://sbi.postech.ac.kr/oasis/introduction/

A tool for various statistical tasks involved in analyzing survival data which provides a uniform platform to facilitate efficient statistical analyses of survival data in the aging field. The statistical features of OASIS include the calculation of Kaplan-Meier estimates, mean/median lifespan, mortality rate, Mantel-Cox Log-Rank test, Fishers exact test, weighted Log-Rank test, Kolmogorov-Smirnov test and Neymans smooth test. Moreover, OASIS generates survival and mortality curves that can be easily exported and modified by using common graphic softwares.

Proper citation: Online Application for Survival Analysis (OASIS) (RRID:SCR_014450) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vdemichev/DiaNN

Software tool for processing of data independent acquisition proteomics experiments. Universal automated software suite for DIA proteomics data analysis. Neural networks and interference correction enable deep proteome coverage in high throughput.

Proper citation: DIA-NN (RRID:SCR_022865) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nextgenusfs/funannotate

Software package for genome annotation. Built specifically for fungi, but will also work with higher eukaryotes. Used for genome prediction, annotation, and comparison.

Proper citation: funannotate (RRID:SCR_023039) Copy   

•   Source: SciCrunch Registry
  

https://github.com/open2c/pairtools

Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments.

Proper citation: pairtools (RRID:SCR_023038) Copy   

•   Source: SciCrunch Registry
  

https://github.com/hartwigmedical/hmftools/blob/master/purple/README.md

Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity.

Proper citation: PURPLE (RRID:SCR_022999) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/de/de/home/technical-resources/technical-reference-library/mass-spectrometry-support-center/liquid-chromatography-mass-spectrometry-software-support/freestyle-software-support/freestyle-software-support-getting-started.html

Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system.

Proper citation: FreeStyle 1.8 SP1 (RRID:SCR_022877) Copy   

•   Source: SciCrunch Registry
  

https://github.com/walaj/svaba

Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.

Proper citation: SvABA (RRID:SCR_022998) Copy   

•   Source: SciCrunch Registry
  

http://www.brainhealthdatabank.ca

Repository of many types and sources of data including, but not limited to, assessments, imaging, wearable, and biological samples, collected from research projects at the Centre for Addiction and Mental Health. Data that individuals choose to share to advance mental health.

Proper citation: BrainHealth Databank (RRID:SCR_022996) Copy   

•   Source: SciCrunch Registry
  

https://sufuorg.com/home.aspx

Organization to optimize the care of women, men, and children with lower urinary tract dysfunction and/or pelvic floor disorders through education, research and involvement in health care policy. To improve the art and science of Urology through basic and applied clinical research in urodynamics and neurourology, voiding function and dysfunction, female urology and pelvic floor dysfunction, and to disseminate and teach these concepts.

Proper citation: Society of Urodynamics, Female Pelvic Medicine and Urogenital Reconstruction (SUFU) (RRID:SCR_022874) Copy   

•   Source: SciCrunch Registry
  

https://labsyspharm.org/

Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials.

Proper citation: Laboratory of Systems Pharmacology program (RRID:SCR_022873) Copy   

•   Source: SciCrunch Registry
  

https://bolin.su.se/data/

Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI.

Proper citation: Bolin Centre Database (RRID:SCR_023142) Copy   

•   Source: SciCrunch Registry
  

https://www.genoscope.cns.fr/brassicanapus/

Web tool as Brassica napus genome browser.

Proper citation: CNS Genoscope (RRID:SCR_023020) Copy   

•   Source: SciCrunch Registry
  

https://www.braincommons.org/

Scalable cloud-based platform for computational discovery designed for the brain health community.The BRAINCommons empowers the global research community by providing access to multi-model data, state-of-the-art tools and a secure interoperable system for data sharing.

Proper citation: BRAIN Commons (RRID:SCR_023140) Copy   

•   Source: SciCrunch Registry
  

https://github.com/c-zhou/yahs

Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.

Proper citation: YaHS (RRID:SCR_022965) Copy   

•   Source: SciCrunch Registry
  

http://www.cbs.dtu.dk/services/SignalP/

Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.

Proper citation: SignalP (RRID:SCR_015644) Copy   

•   Source: SciCrunch Registry
  

https://researchdata.bbk.ac.uk

Repository allows all researchers at Birkbeck to upload data, and get DOI.Data in the Birkbeck Data Repository is stored on Arkivum server.This is a very secure storage space, which will allow our data to remain unchanged and accessible for many years after it is deposited.

Proper citation: Birkbeck Research Data (RRID:SCR_023139) Copy   

•   Source: SciCrunch Registry